New genome sequence of the date palm

In addition, the researchers have identified the genes and mutations that lead to color change and the levels of major sugars in date palm fruit -- including the genes for the enzyme invertase that breaks down sucrose into glucose and fructose. The mapping of these fruit color and sugar genes was conducted using genome-wide association studies (GWAS). GWAS has been used for mapping important disease genes in humans, and this is the first time it has been applied to date palms.

While date palms (Phoenix dactylifera) are one of the earliest domesticated tree crops in the world and remain a major fruit crop in North Africa and the Middle East, few genomic resources exist. This, combined with long generation times, has limited evolutionary genomic studies of this perennial species. In the paper Genome-wide association mapping of date palm fruit traits, published in the journal Nature Communications, the researchers report that they have produced an improved genome assembly for date palms that is 18 percent larger and more contiguous than existing genome assemblies. This long-read genome sequence assembly, coupled with access to two large, mature date palm orchards in the United Arab Emirates, allowed them to conduct genome-wide association mapping in this species. As a result, they successfully mapped the previously-identified sex determination locus and genes for both fruit color and sugar level polymorphisms.

Lead scientist and Silver Professor of Biology, New York University and part of NYU Abu Dhabi Center for Genomics and Systems Biology, Michael Purugganan commented: "As we face challenges in food security for the future, we will need to continue to study the genome of food crops like date palm to help us in our struggle to provide food security in the world. Our progress in expanding the genome of the date palm is finally unlocking some of the secrets that explain how this tree species has continued to thrive in varied, challenging ecosystems."

The sequencing of the date palm genome and the first GWAS mapping in this fruit tree was an international effort led by NYUAD and KCGEB, and also included researchers in the US, Switzerland, France, UK, Saudi Arabia, and Mexico.

Fast facts:

• This new and improved genome sequence, which was published today in the journal Nature Communications, will help scientists explore the genetics of this important food crop, as well as help breeders find new genes to develop new and improved varieties of date palms
• A genome sequence provides the complete genetic code of an organism, and encodes all the genes found in an individual
• Using new single-molecule real time (SMRT) technology, the researchers read a total of more than 772 million genetic letters (or basepairs) of the genetic code of date palms.
• This is currently the most complete genome sequence available for this tree crop
• Using this sequence, the scientists were also able to identify genes for fruit color and sugar content in date palms.

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Journal Reference:

1. Khaled M. Hazzouri, Muriel Gros-Balthazard, Jonathan M. Flowers, Dario Copetti, Alain Lemansour, Marc Lebrun, Khaled Masmoudi, Sylvie Ferrand, Michael I. Dhar, Zoë A. Fresquez, Ulises Rosas, Jianwei Zhang, Jayson Talag, Seunghee Lee, David Kudrna, Robyn F. Powell, Ilia J. Leitch, Robert R. Krueger, Rod A. Wing, Khaled M. A. Amiri, Michael D. Purugganan. Genome-wide association mapping of date palm fruit traits. Nature Communications, 2019; 10 (1) DOI: 10.1038/s41467-019-12604-9